Chemotaxonomy of microorganisms based upon their spectroscopic, spectrometric, and chromatographic characteristics represents a useful method for the identification of microorganisms such as yeast, fungi, protozoa, and bacteria. Typically, such chemotaxonomic methods are based upon instrumental methods that provide “fingerprint” spectra or chromatograms (i.e., spectra or chromatograms that are unique to each type of microorganism). Such fingerprinting methods include mass spectrometric methods (for example, pyrolysis mass spectrometry), infrared spectroscopy, ion mobility spectrometry, gas chromatography, liquid chromatography, nuclear magnetic resonance, and various hyphenated techniques such as gas chromatography-mass spectrometry (GC-MS) and high performance liquid chromatography-Fourier transform infrared spectroscopy (HPLC-FTIR).
Unfortunately, instrumental fingerprinting methods, such as pyrolysis mass spectrometry, tend to suffer from irreproducibility due to both instrumental and environmental factors. For example, continued use of a mass spectrometer leads to contamination of the ion optics and thus can lead to alterations in the appearance of a microorganism's fingerprint mass spectrum. Changes in a microorganism's characteristics due to environmental factors, such as a change in the growth medium used to culture the microorganism, can also alter the appearance of its fingerprint spectrum. Irreproducibility of spectral data due to instrumental and environmental sources makes it difficult to classify or identify microorganisms based on fingerprint spectral patterns. On the other hand, instrumental fingerprinting methods are much more rapid than traditional methods of identifying microorganisms and they hold great potential for detection and identification of biological warfare agents and rapid identification of pathogenic microorganisms in outbreak situations.